# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = DSS1 data-folder = ../eu_basynthec/targets/data # The root directory of the data store storeroot-dir = ${data-folder}/store # The directory for incoming files over rpc rpc-incoming-dir = ${data-folder}/incoming # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8889 # Session timeout in minutes session-timeout = 720 # Set to 'false' for development/testing without deployed server. In this mode datastore will not use # SSL when connecting to openbis. Otherwise all 'keystore' properties need to be set for SSL connection # (default when use-ssl property is not set so there is no need to specify it on production servers). use-ssl = false # Path to the keystore keystore.path = ../datastore_server/dist/etc/openBIS.keystore # Password of the keystore keystore.password = changeit # Key password of the keystore keystore.key-password = changeit # The check interval (in seconds) check-interval = 10 # The time-out for clean up work in the shutdown sequence (in seconds). # Note that that the maximal time for the shutdown sequence to complete can be as large # as twice this time. # Remark: On a network file system, it is not recommended to turn this value to something # lower than 180. shutdown-timeout = 180 # If free disk space goes below value defined here, a notification email will be sent. # Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is # specified or if value is negative, the system will not be watching. highwater-mark = -1 # If a data set is successfully registered it sends out an email to the registrator. # If this property is not specified, no email is sent to the registrator. This property # does not affect the mails which are sent, when the data set could not be registered. notify-successful-registration = false # The URL of the openBIS server server-url = http://localhost:8888 # The username to use when contacting the openBIS server username = etlserver-basynthec # The password to use when contacting the openBIS server password = etlserver # The base URL for Web client access. download-url = http://localhost:${port} # SMTP properties (must start with 'mail' to be considered). # mail.smtp.host = localhost # mail.from = datastore_server@localhost mail.smtp.host = file://targets/playground/email mail.from = datastore_server@localhost # ---------------- Timing parameters for file system operations on remote shares. # Time (in seconds) to wait for any file system operation to finish. Operations exceeding this # timeout will be terminated. timeout = 60 # Number of times that a timed out operation will be tried again (0 means: every file system # operation will only ever be performed once). max-retries = 11 # Time (in seconds) to wait after an operation has been timed out before re-trying. failure-interval = 10 # The period of no write access that needs to pass before an incoming data item is considered # complete and ready to be processed (in seconds) [default: 300]. # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed. quiet-period = 10 # --------------------------------------------------------------------------- # INTERNAL CONFIGURATION, # Do not change this part unless you are developing openBIS extensions. # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- # reporting and processing plugins configuration # --------------------------------------------------------------------------- # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. reporting-plugins = tsv-viewer tsv-viewer.label = Time Series tsv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin # --------------------------------------------------------------------------- # BEGIN DROPBOXES # --------------------------------------------------------------------------- # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' inputs = main-thread, metabolomics, growth-profiles, transcriptomics, proteomics incoming-dir-create = true # --------------------------------------------------------------------------- # main thread configuration # --------------------------------------------------------------------------- main-thread.incoming-dir = ${data-folder}/incoming # Determines when the incoming data should be considered complete and ready to be processed. # Allowed values: # - auto-detection - when no write access will be detected for a specified 'quite-period' # - marker-file - when an appropriate marker file for the data exists. # The default value is 'marker-file'. main-thread.incoming-data-completeness-condition = auto-detection main-thread.delete-unidentified = true main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor main-thread.script-path = ../eu_basynthec/dist/etc/data-set-handler.py main-thread.validation-script-path = ../eu_basynthec/dist/etc/data-set-validator.py # --------------------------------------------------------------------------- # metabolomics thread configuration # --------------------------------------------------------------------------- metabolomics.incoming-dir = ${data-folder}/incoming-metabolomics metabolomics.incoming-data-completeness-condition = auto-detection metabolomics.delete-unidentified = true metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor metabolomics.script-path = ../eu_basynthec/dist/etc/metabolomics2/data-set-handler.py metabolomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/metabolomics2/data-set-validator.py # --------------------------------------------------------------------------- # growth-profiles thread configuration # --------------------------------------------------------------------------- growth-profiles.incoming-dir = ${data-folder}/incoming-od600 growth-profiles.incoming-data-completeness-condition = auto-detection growth-profiles.delete-unidentified = true growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor growth-profiles.script-path = ../eu_basynthec/dist/etc/growth-profiles/data-set-handler.py growth-profiles.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/growth-profiles/data-set-validator.py # --------------------------------------------------------------------------- # transcriptomics thread configuration # --------------------------------------------------------------------------- transcriptomics.incoming-dir = ${data-folder}/incoming-transcriptomics transcriptomics.incoming-data-completeness-condition = auto-detection transcriptomics.delete-unidentified = true transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor transcriptomics.script-path = ../eu_basynthec/dist/etc/transcriptomics/data-set-handler.py transcriptomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/transcriptomics/data-set-validator.py # --------------------------------------------------------------------------- # proteomics thread configuration # --------------------------------------------------------------------------- proteomics.incoming-dir = ${data-folder}/incoming-proteomics proteomics.incoming-data-completeness-condition = auto-detection proteomics.delete-unidentified = true proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor proteomics.script-path = ../eu_basynthec/dist/etc/proteomics/data-set-handler.py proteomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/proteomics/data-set-validator.py # # The dss-rpc section configures the RPC put functionality by providing a mapping between data # set type and input thread parameters. # # The default input thread is specified by the put-default key. If not specified, the first input # thread will be used. # # Mappings are specified by dss-rpc. = # # If this section is empty, then the first input thread will be used. # dss-rpc.put-default = main-thread dss-rpc.put.METABOLITE_INTENSITIES = metabolomics dss-rpc.put.OD600 = growth-profiles dss-rpc.put.TRANSCRIPTOMICS = transcriptomics dss-rpc.put.PROTEIN_QUANTIFICATIONS = proteomics